Johannes Mehserle, right, appears in the East Fork Justice Court on Wednesday, Jan. 14, 2009, in Minden, Nev. Mehserle is being held on charges related to the New Year's day shooting of an unarmed man on an Oakland, Calif., train platform. Mehserle, 27, waived extradition to California early Wednesday during a brief court appearance in Minden, Nev., and was being held without bail on a warrant charging homicide. Douglas County Sheriff's Deputy Ron Mills is at left.

Passengers arriving at the Fruitvale BART station head for the exit in Oakland, Calif., on Thursday, Jan. 29, 2009.

Photo: Paul Chinn, The Chronicle

Passengers arriving at the Fruitvale BART station head for the exit...

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** FILE **This undated family file photo provided by the Law Offices of John Burris shows Oscar Grant, a 22-year-old transit rider who was shot and killed by BART police on New Year's Day, 2009. A Douglas County jail official confirmed that 27-year-old Johannes Mehserle, who was involved in the incident, was in custody Tuesday night, Jan. 14, 2009, under a fugitive warrant issued in California (AP Photo/Family Handout provided by the Law Offices of John Burris) ** NO SALES **

Photo: AP

** FILE **This undated family file photo provided by the Law...

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A train heading for San Francisco pulls into the Fruitvale BART station in Oakland on Thursday, Jan. 29, 2009.

BART's investigation into a police officer's fatal shooting of an unarmed rider was plagued with problems from the start, a Chronicle investigation has found.

BART police allowed a train full of witnesses to pull out of the Fruitvale Station in Oakland early New Year's Day after Officer Johannes Mehserle shot Oscar Grant, then made little effort to contact the witnesses as they got off at other stations.

None of the seven officers at Fruitvale radioed that an officer-involved shooting had taken place. Supervisors sent to the Fruitvale Station initially were in the dark, while officers at stations down the line did not know to expect a train full of witnesses.

A key video showing that another officer on the station platform struck Grant two minutes before he was shot was available to BART, but police did not start a full investigation into the officer's actions until a TV station aired the footage Jan. 23.

BART has failed to provide basic and important information about the case to the public, even while promising transparency. The vacuum has been filled by attorney John Burris, who is seeking $25 million for Grant's family, and by speculation over amateur video footage broadcast on television and the Internet.

BART's response has been hamstrung by the agency's inability to say why Grant was shot as he lay facedown - or even if the shooting was intentional or accidental. BART officials say that is the fault of Mehserle, who refused to speak to criminal investigators and then quit before he was forced to talk to BART's internal affairs division. He has since been charged with murder.

Among the information that BART has withheld is that Grant was shot just after he had been told he was being arrested for resisting an officer, two sources familiar with the investigation told The Chronicle. BART has not said what Grant allegedly did to deserve the arrest.

On Thursday, conceding that they had lost the public's confidence in the investigation, BART officials said they will hire an outside law firm or public agency to decide whether any additional officers should be disciplined, a job normally handled by a police department's internal affairs division.

"Even if we came to the right conclusion," said Joel Keller, a member of the BART Board of Directors, "there would be mistrust."

Chaos on the platform

BART has not discussed what happened on the Fruitvale Station platform in detail. But a Chronicle review that draws on documents, video footage and dozens of interviews paints a picture of a chaotic, complex scene.

About 2 a.m., riders reported a fight as a Dublin-Pleasanton train left the West Oakland station. Grant, 22, of Hayward, was in the train's lead car with his friends after a brief New Year's Eve trip to San Francisco.

BART dispatched officers to Fruitvale to intercept the train. Mehserle, 27, who had been on the BART police force for two years, had to drive with his partner from the West Oakland station. There, a teenage boy with a semiautomatic pistol had fled from police and jumped off the station platform, breaking several bones.

When they got the call about the train fight, Pirone and his partner were downstairs at Fruitvale detaining an alleged drunk. Pirone headed alone up to the platform, where the train was already waiting.

Witnesses who later talked to BART investigators said Pirone, cursing and pointing his Taser, detained Grant and his friends, who had gotten off the train.

A source familiar with the investigation said Grant and another man briefly ran back into the train; Grant then came out voluntarily, while Pirone grabbed Grant's friend and dragged him out.

Pirone took Grant's friend to the platform and handcuffed him, angering some other riders, according to a review of video footage and interviews with several sources close to the investigation.

By now, five other officers, including Mehserle, had joined Pirone and his partner at the station.

Video footage taken with a cell phone aboard the train, and aired last week on KTVU-TV, showed that Pirone suddenly rushed toward Grant as he and two other men stood by a wall near Pirone's partner and struck him. Grant then sat down, the footage shows.

According to two sources familiar with the investigation, Pirone then told Mehserle that Grant and a second man were to be arrested for resisting him.

Mehserle is seen on video footage forcing Grant to his chest and trying to handcuff him before taking out his pistol and firing.

Train pulls out

BART officers soon had the train operator shut the doors and continue east without anyone onboard being interviewed. The officers took the action because they felt they did not have control over increasingly angry riders, said sources familiar with their accounts.

The officers did not announce over their radios that there had been an officer-involved shooting.

According to several sources, a BART lieutenant at the Bay Fair Station in San Leandro obtained critical camera footage from a passenger who had been on the train. The lieutenant, unaware of what was going on, had approached the passenger out of curiosity as the passenger replayed the video.

BART Police Chief Gary Gee confirmed that the train full of witnesses was never stopped or delayed as it moved east from Fruitvale, and as passengers got off at four other stations. Officers who were sent to Dublin, the end of the line, found no witnesses to the shooting, Gee said.

Burris, the attorney for Grant's family, said the failure to announce the shooting over the radio suggested poor training. The delay, he said, "creates more of an opportunity for a coverup."

Mehserle declined to speak to criminal investigators on New Year's Day. It wasn't until Jan. 7 that BART attempted to force him to speak to internal affairs, a delay that police experts called unusual.

Gee and BART General Manager Dorothy Dugger said the focus had been on the criminal investigation and noted that any statement Mehserle gave to internal affairs could not be used to prosecute him in court.

Surprise airing of video

The controversy over Pirone's role erupted last weekend after KTVU aired a key portion of a video it acquired from a passenger soon after Jan. 1.

Although Dugger said BART had considered the TV report to be a "new allegation of unreasonable force," the full, unedited video had been on KTVU's Web site since the afternoon of Jan. 6.

Gee acknowledged Thursday that investigators had seen the footage earlier but said it wasn't conclusive on its own. He also said no one, including Grant's friends, had alleged that Pirone used unreasonable force.

The chief said BART had asked KTVU for a copy of the video early in the investigation and that the station refused to provide one. BART then called Alameda County prosecutors, who went to court to get the video.

Gee said BART still doesn't have a copy of the video, however.

"Until we get an original copy of the KTVU video and we can send it to a forensic lab," Gee said, "we cannot have any degree of certainty as to what happened in that confrontation."

Some BART officials said they felt blindsided when BART was forced into action by a TV station.

"It's embarrassing," said Lynette Sweet, a member of BART's Board of Directors. "The public has been crying out from the beginning, 'What about the other officers on the platform?' "

BART tries to catch up

Increasingly, BART has tried to improve its communications with the public. Officials have held numerous hearings, created a subcommittee of directors that is looking at setting up a civilian review of the police and posted answers to "frequently asked questions" on BART's Web site.

Sweet and fellow Director Tom Radulovich, however, are pushing for the nine-member board to oust Dugger and Gee.

The president of the union representing 236 rank-and-file BART officers said for the first time Thursday that many officers felt there was a "lack of leadership" at the transit agency and had, at a Jan. 22 meeting, discussed whether to hold a no-confidence vote on Gee.

"We as an association are disappointed in management's reactionary response to this entire issue," said union leader Jesse Sekhon. "We expect better leadership."

Dugger defended BART's response, pointing to the fact that prosecutors had charged Mehserle with murder Jan. 13, one day after BART turned over its evidence. She also said she remains confident in Gee.

Gee admitted police could have done a better job discussing the case with members of the media and the public, citing "some communication gaps and lessons learned."

"There's always going to be things we could have done differently," Gee said. He declined to comment on possible mistakes by officers, but said, "If there are any red flags, we will improve on them."

One step that BART is taking: According to documents obtained by The Chronicle, the BART sergeant in charge of the New Year's Day investigation and two of his detectives are scheduled to attend a five-day course next week on investigating officer-involved shootings.